Yes, but cutnb=0 is not acceptable for eneopt=1 ....
Vlad
On 10/25/2013 07:52 PM, Ray Luo, Ph.D. wrote:
> Yes, for nonlinear PB, you have to live with eneopt=1 ... The default
> cutnb = 0 means no cutoff is used.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, and
> Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Fri, Oct 25, 2013 at 10:08 AM, Vlad Cojocaru
> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>> Thanks Ray,
>>
>> Yes ... I figured that out ...
>>
>> Maybe one last question ... The eneopt error came from using the
>> non-linear PB which appears incompatible with eneopt=2.
>>
>> What are the eneopt and cutnb recommendations for non-linear PB ? Would
>> eneopt=1 and cutnb=12 be acceptable or outrageous ?
>>
>> Thanks again
>> Vlad
>>
>> On 10/25/2013 06:56 PM, Ray Luo, Ph.D. wrote:
>>> Vlad,
>>>
>>> The python and perl scripts only accept a very limited set of options
>>> for PBSA. To test with all the options, you have to use PBSA program
>>> directly. Its user interface is like the SANDER program.
>>>
>>> All the best,
>>> Ray
>>> --
>>> Ray Luo, Ph.D.
>>> Professor,
>>> Biochemistry, Molecular Biophysics, and
>>> Biomedical Engineering
>>> University of California, Irvine, CA 92697-3900
>>>
>>>
>>> On Fri, Oct 25, 2013 at 9:02 AM, Vlad Cojocaru
>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>> Dear all,
>>>>
>>>> When using mmpbsa_py_energy in MMPBSA.py and trying to change PBSA
>>>> options in _MMPBSA_pb.mdin, I get lots of weird errors.
>>>> Several options listed as PBSA options in the manual (e.g. ipb, sasopt,
>>>> triopt) are not accepted. Also when I specifically set eneopt = 2 in the
>>>> _MMPBSA_pb.mdin file, the calculation exists with an error saying that
>>>> eneopt = 1 requires a non-zero cutnb as if the input is not read correctly.
>>>>
>>>> I guess given all these problems with mmpbsa_py_energy, it is
>>>> recommended to use sander (by setting use_sander=1)
>>>>
>>>> Best
>>>> Vlad
>>>>
>>>> --
>>>> Dr. Vlad Cojocaru
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Department of Cell and Developmental Biology
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>>>
>>>>
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>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>
>>
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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Oct 25 2013 - 11:30:03 PDT
